abearab / REMBRANDTS

REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability

REMBRANDTS

REMoving Bias from Rna-seq ANalysis of Differential Transcript Stability

REMBRANDTS is a package for analysis of RNA-seq data across multiple samples in order to obtain unbiased estimates of differential mRNA stability. It uses DESeq to obtain estimates of differential pre-mRNA and mature mRNA abundance across samples, and then estimates a gene-specific bias function that is then subtracted from Δexon–Δintron to provide unbiased differential mRNA stability measures.

Requirements

1. Unix-compatible OS
2. R version 3.2.3 or later (tested on 4.3.1)
3. R gplots library
4. R DEseq2 library (previously DESeq)

Installation

REMBRANDTS is ready to use once the Requirements are in place.

Running REMBRANDTS

Input files

For running REMBRANDTS, you need the following files:

• Metadata file. The metadata file is a tab-delimited table with each row corresponding to either the exonic or intronic reads of one sample. The first line contains column headers, which must be exactly the same as follows:

  1. Label. This column contains the sample labels. For example, both the exonic and intronic read sets that come from sample #1 should be labeled as Sample1.
  2. File. This column contains the path to the HTSeq-count output files. The path can be either absolute, or relative to the "inputDir" provided as argument to REMBRANDTS.sh.
  3. ReadType. This column contains the read type for each of the HTSeq-Count files. Should be either intronic or exonic.
  4. Batch. In case batch-specific normalization is required, this column can be used to specify different batches as integer numbers 1 to n, where n is the total number of batches. If batch-specific normalization is not required, this number should always be 1.

  An example metadata table is shown below:

  Label	File	ReadType	Batch
  Sample1	./htseq/Sample1.htseqCount.exonic.tab	exonic	1
  Sample1	./htseq/Sample1.htseqCount.intronic.tab	intronic	1
  Sample2	./htseq/Sample2.htseqCount.exonic.tab	exonic	1
  Sample2	./htseq/Sample2.htseqCount.intronic.tab	intronic	1

• Read count files. In the read count files, each row corresponds to one gene, with the first column representing the gene ID and the second column representing the total number of reads mapped to that gene (either intronic or exonic reads). These files can be generated using HTSeq-count. A complete workflow for generating read count files that are compatible with REMBRENDTS is described here.

Usage

To run REMBRANDTS, use the following command:

bash ./REMBRANDTS.sh <jobID> <metadata.txt> <inputDir> <stringency> <biasMode>

• jobID: A job name that is used to create the output directory.
• inputDir: The directory relative to which the read count file paths are determined.
• stringency: The stringency for determining the cutoff for genes to be included in the analysis. REMBRANDTS determines a read count cutoff that results in an overall Pearson correlation (ρ) between Δexon and Δintron equal to ρ_min+(ρ_max–ρ_min)×stringency.
• biasMode: Currently, only linear is accepted.

Output

REMBRANDTS creates the following output files in ./out/<jobID>/

• exonic.filtered.mx.txt: The estimated log₂ of abundance of exonic fragments (Δexon), relative to the average of all samples.
• exonic.filtered.correl.heatmap.jpg: The heatmap of Pearson similarities of samples with respect to the above estimates.
• intronic.filtered.mx.txt: The estimated log₂ of abundance of intronic fragments (Δintron), relative to the average of all samples.
• intronic.filtered.correl.heatmap.jpg: The heatmap of Pearson similarities of samples with respect to the above estimates.
• stability.filtered.mx.txt: The unbiased estimates of differential mRNA stability (Δexon–Δintron–bias), relative to the average of all samples.
• stability.filtered.correl.heatmap.jpg: The heatmap of Pearson similarities of samples with respect to the above estimates.
• scatterplot.jpg: The scatterplot of Δexon vs. Δintron for all filtered genes in all samples.
• sampleScatterplots/scatterplot.<Label>.jpg: The scatterplot of Δexon–Δintron vs Δintron for each sample, before and after removing the bias term.

Example

Three example datasets are provided in the ./examples/ folder. You can run REMBRANDTS on these examples using these commands:

bash ./REMBRANDTS.sh Human_tissue_stability ./examples/Tissues.SRP056969/table.txt ./examples/Tissues.SRP056969 0.99 linear

bash ./REMBRANDTS.sh AD_stability ./examples/AD.GSE53697/table.txt ./examples/AD.GSE53697 0.7 linear

bash ./REMBRANDTS.sh Mouse_mixed_stability ./examples/Mouse.PMID26098447/table.txt ./examples/Mouse.PMID26098447 0.99 linear

bash ./REMBRANDTS.sh Shen_2012_GSE29278_stability ./examples/Shen_2012_GSE29278_counts/table.txt ./examples/Shen_2012_GSE29278_counts 0.99 linear

bash ./REMBRANDTS.sh Furlow_2015_GSE45162_stability ./examples/Furlow_2015_GSE45162_counts/table.txt ./examples/Furlow_2015_GSE45162_counts 0.99 linear

These commands will replicate the stability estimates presented in Alkallas et al. (Nat Commun, 2017).

Citation

Alkallas R, Fish L, Goodarzi H, Najafabadi HS (2017). Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease. Nat Commun 8:909